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- PDB-8dyb: The crystal structure of the T252A mutant of CYP199A4 bound to 4-... -

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Basic information

Entry
Database: PDB / ID: 8dyb
TitleThe crystal structure of the T252A mutant of CYP199A4 bound to 4-methylthiobenzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Sulfur oxidation / P450 mutant
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
4-methylsulfanylbenzoic acid / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsColeman, T. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Chemistry / Year: 2022
Title: Investigating the Active Oxidants Involved in Cytochrome P450 Catalyzed Sulfoxidation Reactions.
Authors: Podgorski, M.N. / Coleman, T. / Churchman, L.R. / Bruning, J.B. / De Voss, J.J. / Bell, S.G.
History
DepositionAug 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6533
Polymers42,8691
Non-polymers7852
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.914, 50.935, 78.707
Angle α, β, γ (deg.)90.000, 94.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 / CYP199A4


Mass: 42868.633 Da / Num. of mol.: 1 / Mutation: T252A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris HaA2 (phototrophic)
Strain: HaA2 / Gene: RPB_3613 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2IU02
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-4MI / 4-methylsulfanylbenzoic acid


Mass: 168.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 32.2 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: The crystallisation buffer was 100 mM Bis-Tris buffer (adjusted to pH 5.0-5.75 with acetic acid), 0.2 M magnesium acetate and 20-32% PEG 3350
PH range: 5.00-5.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 1, 2017
RadiationMonochromator: Double-crystal Si(111) water-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.88→42.73 Å / Num. obs: 25053 / % possible obs: 99.3 % / Redundancy: 7.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.042 / Rrim(I) all: 0.115 / Net I/σ(I): 11.4 / Num. measured all: 187028 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.88-1.926.90.9311042815030.7240.3721.0051.793.7
9.01-42.736.50.02715892440.9990.0110.0344.798

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.72 Å42.73 Å
Translation5.72 Å42.73 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.29data scaling
PHASER2.7.17phasing
PHENIX1.11.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DO1

4do1


Resolution: 1.88→31.085 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2623 1262 5.06 %
Rwork0.2202 23676 -
obs0.2224 24938 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.66 Å2 / Biso mean: 34.4565 Å2 / Biso min: 12.04 Å2
Refinement stepCycle: final / Resolution: 1.88→31.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3019 0 54 164 3237
Biso mean--21.35 33.52 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043172
X-RAY DIFFRACTIONf_angle_d0.7124336
X-RAY DIFFRACTIONf_chiral_restr0.042470
X-RAY DIFFRACTIONf_plane_restr0.005577
X-RAY DIFFRACTIONf_dihedral_angle_d16.8631896
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.88-1.95490.35771330.309246294
1.9549-2.04380.31351410.2953261299
2.0438-2.15160.31271390.27182624100
2.1516-2.28630.29291220.24852647100
2.2863-2.46280.29151430.25052647100
2.4628-2.71050.28111240.23782640100
2.7105-3.10240.27541540.222654100
3.1024-3.90750.24151450.19022686100
3.9075-31.0850.21831610.17932704100

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